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Energy transport dynamics in different nanostructures are crucial to both fundamental understanding and practical applications for heat management at the nanoscale. It has been reported that thermal conductivity may be severely impacted by stacking disorder in layered materials. Here, using ultrafast electron diffraction in the reflection geometry for direct probing of structural dynamics, we report a fundamental behavioral difference due to stacking order in an entirely different system—solid-supported methanol assemblies whose layered structures may resemble those of two-dimensional (2D) and van der Waals (vdW) solids but with much weaker in-plane hydrogen bonds. Thermal diffusion is found to be the transport mechanism across 2D-layered films without a cross-plane stacking order. In stark contrast, much faster ballistic energy transport is observed in 3D-ordered crystalline solids. The major change in such dynamical behavior may be associated with the efficiency of vibrational coupling between vdW-interacted methanol layers, which demonstrates a strong structure‒property relation.